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<title>Per Base Sequence Content</title>
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<h1>Per Base Sequence Content</h1>
<h2>Summary</h2>
<p>
Per Base Sequence Content plots out the proportion of each base
position in a file for which each of the four normal DNA bases
has been called.
</p>
<p><img src="per_base_sequence_content.png"></p>
<p>
In a random library you would expect that there would be little
to no difference between the different bases of a sequence run, so
the lines in this plot should run parallel with each other.  The
relative amount of each base should reflect the overall amount of
these bases in your genome, but in any case they should not be
hugely imbalanced from each other.
</p>
<p>
It's worth noting that some types of library will always produce biased
sequence composition, normally at the start of the read.  Libraries 
produced by priming using random hexamers (including nearly all RNA-Seq libraries)
and those which were fragmented using transposases inherit an intrinsic
bias in the positions at which reads start. This bias does not concern 
an absolute sequence, but instead provides enrichement of a number of 
different K-mers at the 5' end of the reads.  Whilst this is a true
technical bias, it isn't something which can be corrected by trimming
and in most cases doesn't seem to adversely affect the downstream analysis.
It will however produce a warning or error in this module.
</p>

<h2>Warning</h2>
<p>
This module issues a warning if the difference between A and T, or G
and C is greater than 10% in any position.
</p>

<h2>Failure</h2>
<p>
This module will fail if the difference between A and T, or G and C
is greater than 20% in any position.
</p>

<h2>Common reasons for warnings</h2>
<p>
There are a number of common scenarios which would ellicit a warning 
or error from this module.
</p>

<ol>
<li>Overrepresented sequences: If there is any evidence of overrepresented
sequences such as adapter dimers or rRNA in a sample then these sequences 
may bias the overall composition and their sequence will emerge from this plot.
<li>Biased fragmentation: Any library which is generated based on the ligation
of random hexamers or through tagmentation should theoretically have good
diversity through the sequence, but experience has shown that these libraries 
always have a selection bias in around the first 12bp of each run.  This is
due to a biased selection of random primers, but doesn't represent any individually
biased sequences.  Nearly all RNA-Seq libraries will fail this module because of
this bias, but this is not a problem which can be fixed by processing, and it 
doesn't seem to adversely affect the ablity to measure expression.
<li>Biased composition libraries: Some libraries are inherently biased in their
sequence composition.  The most obvious example would be a library which has been 
treated with sodium bisulphite which will then have converted most of the cytosines
to thymines, meaning that the base composition will be almost devoid of cytosines 
and will thus trigger an error, despite this being entirely normal for that type of
library</li>
<li>If you are analysing a library which has been aggressivley adapter trimmed 
then you will naturally introduce a composition bias at the end of the reads as 
sequences which happen to match short stretches of adapter are removed, leaving 
only sequences which do not match.  Sudden deviations in composition at the end
of libraries which have undergone aggressive trimming are therefore likely to be
spurious.</li>

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